BN1221 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 1.6508e-07 3.9576e-06
Layer 3 3.9407e-07 4.4029e-04
Layer 5 7.1207e-06 9.1090e-05
Layer 6 9.2151e-06 6.7901e-04
Layer 2 5.4177e-05 9.9054e-03
WM 7.4100e-03 1.2919e-01
Layer 1 9.9988e-01 9.3420e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
UBE2V2 Expression Distribution
Gene Specificity Score (GSS)
UBE2V2 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
UBE2V2 Layer 4 3.1426 0.8460
MAPK9 Layer 4 3.1738 0.8435
MOAP1 Layer 5 3.1875 0.8433
HPCA Layer 4 4.4219 0.8419
KLC2 Layer 4 3.1904 0.8372
NSG1 Layer 4 3.5781 0.8349
LYSMD2 Layer 4 3.0225 0.8342
L1CAM Layer 4 3.2578 0.8332
CLSTN3 Layer 4 2.9932 0.8329
CPLX1 Layer 5 3.6992 0.8327
NRSN2 Layer 4 2.9502 0.8326
PFKM Layer 5 3.0312 0.8324
RIMS3 Layer 4 3.8535 0.8318
MYO5A Layer 4 3.5059 0.8317
SCN1B Layer 4 3.8252 0.8308
MARCKS Layer 5 3.0312 0.8307
CADM2 Layer 4 2.8828 0.8300
DYNLT3 Layer 5 3.1797 0.8300
DDX1 Layer 5 2.7012 0.8299
BCAP29 Layer 5 2.9414 0.8298
EPDR1 Layer 5 3.0918 0.8288
TUBB3 Layer 5 3.4688 0.8286
NAP1L5 Layer 5 3.4082 0.8286
KLHDC3 Layer 4 2.9922 0.8282
UBE2V1 Layer 4 2.7422 0.8272
ATP5F1C Layer 4 2.7969 0.8270
GABRG2 Layer 4 3.4980 0.8268
KCNA2 Layer 4 3.7246 0.8267
HABP4 Layer 4 2.7539 0.8265
ATP6V1A Layer 5 3.5742 0.8263
OXR1 Layer 5 3.1738 0.8261
COX7A2L Layer 5 2.8516 0.8254
AAK1 Layer 4 3.0654 0.8253
SORL1 Layer 5 2.9082 0.8251
LDB2 Layer 4 3.1797 0.8249
ABHD8 Layer 4 3.6055 0.8246
NUAK1 Layer 4 3.4746 0.8245
VDAC3 Layer 4 2.8145 0.8244
GOT1 Layer 4 3.3438 0.8242
MAGED1 Layer 4 2.7969 0.8241
NARS Layer 4 2.7754 0.8239
KCNC2 Layer 4 3.7969 0.8237
ARHGDIG Layer 5 3.2637 0.8236
CISD1 Layer 4 2.8457 0.8233
SULT4A1 Layer 4 3.5820 0.8233
ASPH Layer 4 3.3467 0.8232
UBE2E3 Layer 4 3.3496 0.8232
BEX5 Layer 5 3.2363 0.8232
VPS35 Layer 4 3.1152 0.8229
CAP2 Layer 4 3.2324 0.8228

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1221
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1221_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1221/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1221/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1221/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1221/report/PD/BN1221_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1221/report/PD/BN1221_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 02:56:01
  • Number of Processes: 10
  • Spending Time: 0h 2m